From d66bd4aa0bf9c4d9b8793a4e308c9e80691b440f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Nov 2023 21:40:01 +0100 Subject: Enable links to source, upgrade to bootstrap 5 --- docs/reference/GUS.html | 341 +++++++++++++++++++----------------------------- 1 file changed, 137 insertions(+), 204 deletions(-) (limited to 'docs/reference/GUS.html') diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index e371c1a..d2aa03b 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -1,251 +1,184 @@ - - - - - - - -Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$">Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm + Skip to contents + +
+
+
+

Groundwater ubiquity score based on Gustafson (1989)

+ Source: R/GUS.R +
GUS.Rd
-
+

The groundwater ubiquity score GUS is calculated according to the following equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$

- 
GUS(...)
-
-# S3 method for numeric
-GUS(DT50, Koc, ...)
-
-# S3 method for chent
-GUS(
-  chent,
-  degradation_value = "DT50ref",
-  lab_field = "laboratory",
-  redox = "aerobic",
-  sorption_value = "Kfoc",
-  degradation_aggregator = geomean,
-  sorption_aggregator = geomean,
-  ...
-)
-
-# S3 method for GUS_result
-print(x, ..., digits = 1)
- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
...

Included in the generic to allow for further arguments later. Therefore -this also had to be added to the specific methods.

DT50

Half-life of the chemical in soil. Should be a field +

+

Usage

+ 
GUS(...)
+
+# S3 method for numeric
+GUS(DT50, Koc, ...)
+
+# S3 method for chent
+GUS(
+  chent,
+  degradation_value = "DT50ref",
+  lab_field = "laboratory",
+  redox = "aerobic",
+  sorption_value = "Kfoc",
+  degradation_aggregator = geomean,
+  sorption_aggregator = geomean,
+  ...
+)
+
+# S3 method for GUS_result
+print(x, ..., digits = 1)
+
+ +
+

Arguments

+
...
+

Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.

+ + +
DT50
+

Half-life of the chemical in soil. Should be a field half-life according to Gustafson (1989). However, leaching to the sub-soil can not completely be excluded in field dissipation experiments and Gustafson did not refer to any normalisation procedure, but says the field study should -be conducted under use conditions.

Koc

The sorption constant normalised to organic carbon. Gustafson +be conducted under use conditions.

+ + +
Koc
+

The sorption constant normalised to organic carbon. Gustafson does not mention the nonlinearity of the sorption constant commonly found and usually described by Freundlich sorption, therefore it is unclear at which reference concentration the Koc should be observed -(and if the reference concentration would be in soil or in porewater).

chent

If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below.

degradation_value

Which of the available degradation values should -be used?

lab_field

Should laboratory or field half-lives be used? This +(and if the reference concentration would be in soil or in porewater).

+ + +
chent
+

If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.

+ + +
degradation_value
+

Which of the available degradation values should +be used?

+ + +
lab_field
+

Should laboratory or field half-lives be used? This defaults to lab in this implementation, in order to avoid double-accounting for mobility. If comparability with the original GUS values given by Gustafson (1989) is desired, non-normalised first-order -field half-lives obtained under actual use conditions should be used.

redox

Aerobic or anaerobic degradation data

sorption_value

Which of the available sorption values should be used? +field half-lives obtained under actual use conditions should be used.

+ + +
redox
+

Aerobic or anaerobic degradation data

+ + +
sorption_value
+

Which of the available sorption values should be used? Defaults to Kfoc as this is what is generally available from the European pesticide peer review process. These values generally use a reference concentration of 1 mg/L in porewater, that means they would be expected to -be Koc values at a concentration of 1 mg/L in the water phase.

degradation_aggregator

Function for aggregating half-lives

sorption_aggregator

Function for aggregation Koc values

x

An object of class GUS_result to be printed

digits

The number of digits used in the print method

- -

Value

- -

A list with the DT50 and Koc used as well as the resulting score - of class GUS_result

-

References

+be Koc values at a concentration of 1 mg/L in the water phase.

+ + +
degradation_aggregator
+

Function for aggregating half-lives

+ + +
sorption_aggregator
+

Function for aggregation Koc values

+ +
x
+

An object of class GUS_result to be printed

+ + +
digits
+

The number of digits used in the print method

+ +
+
+

Value

+ + +

A list with the DT50 and Koc used as well as the resulting score + of class GUS_result

+
+
+

References

Gustafson, David I. (1989) Groundwater ubiquity score: a simple method for assessing pesticide leachability. Environmental toxicology and chemistry 8(4) 339–57.

- -
- +
+

Author

Johannes Ranke

-
-
+
+ + - + - - - + -- cgit v1.2.3 From 4079a2c496aa4e8c6dc2a93afedcbedbf7a852b5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Nov 2023 21:59:34 +0100 Subject: Enable markdown and rebuild docs --- DESCRIPTION | 1 + docs/pkgdown.yml | 2 +- docs/reference/EFSA_washoff_2017.html | 8 ++-- docs/reference/FOCUS_GW_scenarios_2012.html | 12 +++--- docs/reference/FOCUS_Step_12_scenarios.html | 6 +-- docs/reference/FOMC_actual_twa.html | 4 +- docs/reference/GUS.html | 6 +-- docs/reference/PEC_soil.html | 40 +++++++++--------- docs/reference/PEC_sw_drainage_UK.html | 10 ++--- docs/reference/PEC_sw_drift.html | 2 +- docs/reference/PEC_sw_exposit_drainage.html | 14 +++---- docs/reference/PEC_sw_exposit_runoff.html | 14 +++---- docs/reference/PEC_sw_focus.html | 28 ++++++------- docs/reference/SFO_actual_twa.html | 4 +- docs/reference/SSLRC_mobility_classification.html | 12 +++--- docs/reference/TOXSWA_cwa.html | 32 +++++++++++++-- docs/reference/TSCF-1.png | Bin 27659 -> 40587 bytes docs/reference/TSCF.html | 6 +-- docs/reference/endpoint.html | 12 +++--- docs/reference/max_twa.html | 8 ++-- docs/reference/perc_runoff_exposit.html | 14 +++---- docs/reference/perc_runoff_reduction_exposit.html | 8 ++-- docs/reference/soil_scenario_data_EFSA_2015.html | 26 ++++++------ docs/reference/soil_scenario_data_EFSA_2017.html | 26 ++++++------ docs/search.json | 2 +- man/EFSA_washoff_2017.Rd | 8 ++-- man/FOCUS_GW_scenarios_2012.Rd | 8 ++-- man/FOCUS_Step_12_scenarios.Rd | 6 +-- man/FOMC_actual_twa.Rd | 4 +- man/GUS.Rd | 6 +-- man/PEC_soil.Rd | 48 +++++++++++----------- man/PEC_sw_drainage_UK.Rd | 12 +++--- man/PEC_sw_drift.Rd | 2 +- man/PEC_sw_exposit_drainage.Rd | 14 +++---- man/PEC_sw_exposit_runoff.Rd | 14 +++---- man/PEC_sw_focus.Rd | 28 ++++++------- man/SFO_actual_twa.Rd | 4 +- man/SSLRC_mobility_classification.Rd | 14 +++---- man/TOXSWA_cwa.Rd | 6 +-- man/TSCF.Rd | 2 +- man/endpoint.Rd | 12 +++--- man/max_twa.Rd | 8 ++-- man/perc_runoff_exposit.Rd | 18 ++++---- man/perc_runoff_reduction_exposit.Rd | 14 +++---- man/soil_scenario_data_EFSA_2015.Rd | 18 ++++---- man/soil_scenario_data_EFSA_2017.Rd | 18 ++++---- 46 files changed, 290 insertions(+), 271 deletions(-) (limited to 'docs/reference/GUS.html') diff --git a/DESCRIPTION b/DESCRIPTION index a12f90b..a159c56 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -27,4 +27,5 @@ LazyLoad: yes LazyData: yes Encoding: UTF-8 URL: https://pkgdown.jrwb.de/pfm, https://github.com/jranke/pfm +Roxygen: list(markdown = TRUE, r6 = TRUE) RoxygenNote: 7.2.3 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index eeed6da..6571239 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.17.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2023-11-12T20:34Z +last_built: 2023-11-12T20:59Z urls: reference: https://pkgdown.jrwb.de/pfm/reference article: https://pkgdown.jrwb.de/pfm/articles diff --git a/docs/reference/EFSA_washoff_2017.html b/docs/reference/EFSA_washoff_2017.html index 1e292af..b424de9 100644 --- a/docs/reference/EFSA_washoff_2017.html +++ b/docs/reference/EFSA_washoff_2017.html @@ -54,10 +54,10 @@

Source

European Food Safety Authority (2017) EFSA guidance document for - predicting environmental concentrations of active substances of plant - protection products and transformation products of these active substances - in soil. EFSA Journal 15(10) 4982 - doi:10.2903/j.efsa.2017.4982

+predicting environmental concentrations of active substances of plant +protection products and transformation products of these active substances +in soil. EFSA Journal 15(10) 4982 +doi:10.2903/j.efsa.2017.4982

diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 84c2fac..2e9982b 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -1,6 +1,6 @@ -A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfmA very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfmProperties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfmProperties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfmProperties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm